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International audience; Marker informed breeding could be a favorable opportunity to accelerate cultivar selection in poplar. Linking genotype to phenotypic variation of important economical and adaptive traits is the prerequisite. The two strategies chosen are QTL detection in mapping pedigrees and association studies in natural populations. An intra-specific mapping pedigree Populus nigra x P. nigra of 300 individuals segregating for leaf rust resistance is available. Another large progeny of 1400 individuals derived from a cross P. deltoides x P. trichocarpa for which two major factors and QTL of rust resistance segregated is already available. QTL for phenology and water use efficiency were also mapped. Large scale phenotyping of wood properties is underway. An association mapping population of 1100 P. nigra individuals coming from France, Germany, Netherlands and Spain was evaluated for rust resistance in both controlled and field conditions. Even if most of the genetic variation for rust resistance could be observed at the genotype level, significant differentiation between natural populations was detected. Taking advantages of genomics development in poplar including structural and functional genomics, positional, functional and expressional candidate genes were identified for rust resistance, phenology and wood properties. It became clear that SNP in those genes could be ideal combined to HTP genotyping technologies to identify causative polymorphism for phenotypic variation. We developed collections of SNP useful for both genetic and association mapping. With the help of the genome sequence, unique primer pairs were automatically designed and tested for their uniqueness before PCR amplification and HTP Sanger re-sequencing. Based on the analysis of 850 gene fragments, an average of 1SNP/90bp were found in the three Populus species studied. SNP appeared fixed in each species after comparison of SNP position between the three species. Analysis of linkage disequilibrium in P. nigra showed a rapid decline of LD with physical distance

Association studies aim at linking phenotypic variation with allelic variation in candidate genes and benefit from several generations of recombination in natural populations to identify causative polymorphisms. Such association studies are under development on Populus nigra L., with emphasis on nucleotide polymorphism associated to quantitative resistance to Melampsora larici-populina Kleb (Mlp), the causal agent of leaf rust. Populus nigra, the natural host of Mlp, is widely represented in European riparian ecosystems, where the occurrence and impact of the fungus are highly variable. Geographical patterns of nucleotide diversity in genes involved in the host-pathogen interaction is expected from local co-evolution. As a first step, Single Nucleotide Polymorphisms (SNPs) have been identified in a discovery panel of twenty-one P. nigra genotypes covering French natural range. Sequencing was done on both functional and positional candidate resistance genes (closeness to mapped QTLs and resistance genes). An automated procedure for primer design allowed us to obtain successful amplification in P. nigra for 90% of gene fragments. Average nucleotide variation in P. nigra is high (1 SNP/97 pb). A collection of more than 1100 P. nigra genotypes collected in different natural populations mainly in France but also in Germany, Netherlands, Italy and Spain was evaluated for rust resistance under natural inoculation in a clonal test in France and under artificial inoculations with different strains in leaf-disk bioassays. Even if most of the genetic variation for rust resistant could be observed at the individual (genotype) level, significant differentiation between natural populations was detected. The high level of genetic diversity observed at both gene and phenotypic levels, the rapid linkage disequilibrium decay between SNP is offering a favourable situation to identify interesting resistance alleles and to avoid false positive associations.

International audience; High levels of variability for partial resistance to Melampsora larici-populina leaf rust in black poplar (Populus nigra L.) across Europe offers unique opportunity to identify favourable alleles through association studies. Nucleotide polymorphism (SNP and indels) within candidate genes has been explored in a discovery panel of 21 French P.nigra genotypes. Phenotyping for field and laboratory resistance components revealed significant diversity at both the intra and inter-metapopulation levels, with a suspected North vs. South geographical contrast.

National audience; Foliar rust is the most devastating disease affecting European poplar plantations. One major QTL (Rus), identified in a Populus deltoides x P. trichocorpa pedigree, is on the process of positional cloning. To precise the molecular basis of Rus, joint proteomic and transcriptomic approaches were used to characterize differential expression 2 and 4 days post inoculation (dpi) in two bulks (Rus vs rus) of 10 progenies. At 2 dpi, few transcripts showed an altered expression in the Rus bulk, while genes known to be targeted by resistance genes in plant pathosystems, were found up-regulated 4 dpi. The rus bulk did not present such gene up-regulation while several transcripts, including defense-related genes, were down-regulated as early as 2 dpi. Changes in the proteome were studied by 2-D PAGE analysis and MS/MS characterization of a selected subset of 50 protein spots at 2 and 4 dpi. Interestingly, the proteins overexpressed in the Rus genotypes correlated quite well with the transcriptomic data. All the results, including data coming from positional cloning, suggested that Rus activates the same genes than those involved in qualitative resistance, but this activation is delayed in the quantitative response.

National audience

International audience; The seasonal cycle of growth and dormancy is a distinct character of perennial plants and represents one of the most basic adaptations of trees to their environment. The recurrent transitions of meristems into and out of dormancy are of primary significance to plant productivity and survival. These transitions are tightly linked to the yearly dates of bud flush and bud set that in turn delimit the growth season. ln poplar, perception of a short-day signal leads to apical bud set and dormancy induction. Because bud set is of prime importance in determining season length in a changing environment, we dissected this developmental program at the phenotypical, genetical and molecular levels. Taking advantage of the poplar genome sequence, we integrate candidate genes obtained in large-scale gene expression studies with information of QTLs determined in three poplar pedigrees. Expressional candidate genes were identified in the apex/bud during short-day-induced bud set, using cDNA-AFLP and micro-arrays. Apical buds of plants were sampled at weekly intervals during six weeks of short days, after which apical buds are fully dormant and cannot resume growth without prior cold treatment. The set of significantly differentially expressed genes comprises 1350 genes. For phenotypic measurements in the field, a new bud-set scoring system was developed: bud set is phenotyped with seven developmentally distinct stages. This system allows accounting for the onset of the bud-set process as weil as for its dynamics, as opposed to most earlier studies that rely on the date of accomplished bud set only. Applying this system, high-resolution phenotypic data were obtained in three poplar pedigrees, grown in two environments, and a collection of 450 Populus nigra accessions. QTLs for different bud-set-related traits have been determined in the three pedigrees and have been positioned onto the poplar genome sequence. Integrated with the position of the expressional candidate genes, they identify genomic regions of relevance for bud set. Together, this integrated approach provides a comprehensive overview of bud set in terms of the molecular processes associated with aspects of bud development and elucidates the genetic architecture of bud set. Genes or genomic regions identified through this combined approach are tested for their adaptive relevance in association genetics approaches (see abstract of Zaina et al.).